<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>MolTK C++ API: Class Members</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>
<link href="doxygen.css" rel="stylesheet" type="text/css" />

<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
  $(document).ready(function() { searchBox.OnSelectItem(0); });
</script>

</head>
<body>
<div id="top"><!-- do not remove this div! -->


<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  
  <td id="projectlogo"><img alt="Logo" src="moltk55.png"/></td>
  
  
  <td style="padding-left: 0.5em;">
   <div id="projectname">MolTK C++ API
   &#160;<span id="projectnumber">0.4.0</span>
   </div>
   
  </td>
  
  
  
 </tr>
 </tbody>
</table>
</div>

<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
  <div id="navrow1" class="tabs">
    <ul class="tablist">
      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
      <li><a href="files.html"><span>Files</span></a></li>
      <li>
        <div id="MSearchBox" class="MSearchBoxInactive">
        <span class="left">
          <img id="MSearchSelect" src="search/mag_sel.png"
               onmouseover="return searchBox.OnSearchSelectShow()"
               onmouseout="return searchBox.OnSearchSelectHide()"
               alt=""/>
          <input type="text" id="MSearchField" value="Search" accesskey="S"
               onfocus="searchBox.OnSearchFieldFocus(true)" 
               onblur="searchBox.OnSearchFieldFocus(false)" 
               onkeyup="searchBox.OnSearchFieldChange(event)"/>
          </span><span class="right">
            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
          </span>
        </div>
      </li>
    </ul>
  </div>
  <div id="navrow2" class="tabs2">
    <ul class="tablist">
      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
      <li><a href="inherits.html"><span>Class&#160;Hierarchy</span></a></li>
      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
    </ul>
  </div>
  <div id="navrow3" class="tabs2">
    <ul class="tablist">
      <li class="current"><a href="functions.html"><span>All</span></a></li>
      <li><a href="functions_func.html"><span>Functions</span></a></li>
      <li><a href="functions_vars.html"><span>Variables</span></a></li>
      <li><a href="functions_type.html"><span>Typedefs</span></a></li>
      <li><a href="functions_enum.html"><span>Enumerations</span></a></li>
      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
      <li><a href="functions_rela.html"><span>Related&#160;Functions</span></a></li>
    </ul>
  </div>
  <div id="navrow4" class="tabs3">
    <ul class="tablist">
      <li><a href="functions.html#index_a"><span>a</span></a></li>
      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
      <li class="current"><a href="functions_0x67.html#index_g"><span>g</span></a></li>
      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
      <li><a href="functions_0x6b.html#index_k"><span>k</span></a></li>
      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
      <li><a href="functions_0x71.html#index_q"><span>q</span></a></li>
      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
      <li><a href="functions_0x73.html#index_s"><span>s</span></a></li>
      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
    </ul>
  </div>
</div>
<div class="contents">
<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>

<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
<li>g
: <a class="el" href="classmoltk_1_1Aligner_1_1Cell.html#ac66f132d15e84f948a4b041d78c56f03">moltk::Aligner::Cell</a>
</li>
<li>gap_extension_penalty
: <a class="el" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a8e918b0d431d48be6d8f5dcbd9294093">moltk::MatrixScorer::QueryPosition</a>
, <a class="el" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a2bf28e7f278dc41a844eeb17067be4bb">moltk::MatrixScorer::TargetPosition</a>
</li>
<li>gap_open_penalty
: <a class="el" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a58acc0c7df51b60ffcf81ef1182574df">moltk::MatrixScorer::QueryPosition</a>
, <a class="el" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ae29d8a56f5c10b484d754b79d9d1b8ea">moltk::MatrixScorer::TargetPosition</a>
</li>
<li>get_blosum62_scorer()
: <a class="el" href="classmoltk_1_1MatrixScorer.html#a58a29032f0c197845d1c1cabb4bf2d84">moltk::MatrixScorer</a>
</li>
<li>get_default_scorer()
: <a class="el" href="classmoltk_1_1Aligner.html#a7d364467fa46629a81c3adbcc2cd2692">moltk::Aligner</a>
</li>
<li>get_description()
: <a class="el" href="classmoltk_1_1Biosequence.html#a8290cae93ff500228664fbb4666777a3">moltk::Biosequence</a>
</li>
<li>get_end_gaps_free()
: <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html#a3a2423f141a527da14a45f1a19155333">moltk::Aligner::Scorer</a>
, <a class="el" href="classmoltk_1_1Aligner.html#aeb69db8c0ba583694b389d37e2f9f05b">moltk::Aligner</a>
</li>
<li>get_estring()
: <a class="el" href="classmoltk_1_1Alignment.html#a68e0607cad31d5eec46b90d81c62eed2">moltk::Alignment</a>
</li>
<li>get_gap_extension_penalty()
: <a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html#a466b25d8775b6b874bcc3156f28070fe">moltk::Aligner::QueryPosition</a>
, <a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html#aaf13d881d1b6fab6b27ad31df722d70f">moltk::Aligner::TargetPosition</a>
, <a class="el" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a6dd13920fe7322b872381e6d2f80f3ad">moltk::MatrixScorer::QueryPosition</a>
, <a class="el" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a78d5d85f2e0502eee87c28e6b0b969d5">moltk::MatrixScorer::TargetPosition</a>
</li>
<li>get_gap_open_penalty()
: <a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html#a91e7d5b5631000c409593281abb9ee19">moltk::Aligner::QueryPosition</a>
, <a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html#a7327d83dc678f6c8970e07f50a15cbdd">moltk::Aligner::TargetPosition</a>
, <a class="el" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a2dca485364b5b80dbc0a77ffe20af16a">moltk::MatrixScorer::QueryPosition</a>
, <a class="el" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a763d419002cf6f6c2fca59d93391e945">moltk::MatrixScorer::TargetPosition</a>
</li>
<li>get_instance()
: <a class="el" href="structmoltk_1_1units_1_1Unit.html#a826fc8257f93873c15845a01e465dfc3">moltk::units::Unit&lt; D &gt;</a>
</li>
<li>get_number_of_columns()
: <a class="el" href="classmoltk_1_1Alignment.html#a628e15ff3478f591868bc1465109b04d">moltk::Alignment</a>
</li>
<li>get_number_of_residues()
: <a class="el" href="classmoltk_1_1Biosequence.html#ac990688fe005304a3dd512a616017c71">moltk::Biosequence</a>
, <a class="el" href="classmoltk_1_1BaseBiosequence.html#a837f45a8604c435855b00aa90ace5841">moltk::BaseBiosequence</a>
, <a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html#acbde49bcc732f9830a3c1d60e37c0644">moltk::PDBStructure::Chain</a>
</li>
<li>get_number_of_sequences()
: <a class="el" href="classmoltk_1_1Alignment.html#a2486341695c895251bd124357a21371c">moltk::Alignment</a>
</li>
<li>get_one_letter_code()
: <a class="el" href="classmoltk_1_1PDBStructure_1_1Residue.html#aed00039c0a6da6e4e5a83d23ec898c98">moltk::PDBStructure::Residue</a>
, <a class="el" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#aca9c851b8f3d46dfe93ff6a316a51c59">moltk::BaseBiosequence::BaseResidue</a>
, <a class="el" href="classmoltk_1_1BiosequenceResidue.html#a3bcbd7c24c5df4fa8d6b5e64c77ea136">moltk::BiosequenceResidue</a>
</li>
<li>get_record_type()
: <a class="el" href="classmoltk_1_1PDBStructure_1_1Atom.html#a2284676e8460e244b9ac326a19b3e34f">moltk::PDBStructure::Atom</a>
</li>
<li>get_residue()
: <a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html#a24980b95a88bb1476c283a6f91944a2c">moltk::PDBStructure::Chain</a>
, <a class="el" href="classmoltk_1_1Biosequence.html#a7347126c11c30536dfc3b0214f0dcc44">moltk::Biosequence</a>
, <a class="el" href="classmoltk_1_1BaseBiosequence.html#ae966c9bf162db00c2d5a4898170538af">moltk::BaseBiosequence</a>
</li>
<li>get_residue_number()
: <a class="el" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html#a21a653fddb38c2312eeca3f197e6bbc8">moltk::BaseBiosequence::BaseResidue</a>
, <a class="el" href="classmoltk_1_1BiosequenceResidue.html#ad7a50af311f8d4d088fb2367e456569f">moltk::BiosequenceResidue</a>
, <a class="el" href="classmoltk_1_1PDBStructure_1_1Residue.html#a95335a7d300e9821bdbffb7b3a35060e">moltk::PDBStructure::Residue</a>
</li>
<li>get_sequence()
: <a class="el" href="classmoltk_1_1Alignment.html#aa27d71c83a6cb5d0584e9db931119045">moltk::Alignment</a>
</li>
<li>get_shared_aligner()
: <a class="el" href="classmoltk_1_1Aligner.html#a2a94cf962985576ec14640ee519fa371">moltk::Aligner</a>
</li>
</ul>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Friends</a></div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>



<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.7.5.1
</small></address>

</body>
</html>
